UCSC Genome Browser · Tutorial 4

Clinical case studies

Real diagnostic variants, worked live on the Browser

Coding · splicing · non-coding · structural & repeat · genome.ucsc.edu

How these case studies work

Each case is a real diagnostic variant saved as a live UCSC session — open it and follow along.
Each case is a real diagnostic variant saved as a live UCSC session, so you can open it and follow along.
They are grouped by variant class: coding, splicing, non-coding/regulatory, and structural/repeat.
The recurring move: pick the right Recommended Track Set, then read the evidence off the stacked tracks.
Cases contributed by clinical collaborators (credited per slide); sessions are public.

Builds on Tutorial 3 Tutorial 3 introduced the tracks and Recommended Track Sets; here we put them to work on one variant after another.

Coding variants

read the call — then check the transcript

read the call, then check the transcript

MECP2 — Rett syndrome

MECP2: Rett syndrome

NM_001110792.2(MECP2):c.538C>T p.Arg180Ter (R168X) chrX

X-linked neurodevelopmental disorder; a classic loss-of-function nonsense variant.
You can paste the HGVS expression straight into the position box and press Enter.

Read it off the set Load the Clinical SNVs Recommended Track Set: ClinVar, HGMD and LOVD stack the pathogenic evidence at the codon.

Try it, ▶ open the session Paste the HGVS, then open Recommended Track Sets → Clinical SNVs.

Session: s/Max/rett

MECP2 Rett-syndrome nonsense variant on hg38 — MECP2 nonsense variant with ClinVar / HGMD / LOVD tracks

MAP2K2 — a small missense

MAP2K2: a small missense

NM_030662.4(MAP2K2):c.401A>G p.Tyr134Cys

A RASopathy-gene missense change — the everyday coding question.
The SNV Recommended Track Set is on display here.

A RASopathy-gene missense change, the everyday coding question.
The SNV Recommended Track Set is on display here.

Lines of evidence ClinVar submitted interpretations & evidence, plus Varaico literature annotations for Y134C, sit together in one view.

Try it, ▶ open the session Read the ClinVar interpretations and the Varaico annotation for Y134C.

Example session (variant via Marina Di Stefano, Broad Institute)

Variant via Marina Di Stefano, Broad Institute

MAP2K2 c.401A>G missense on hg38 — MAP2K2 Y134C missense with SNV Recommended Track Set

Read the annotation carefully

when a coding call isn't what it seems

TCF4 — but do you trust this exon?

TCF4, but do you trust this exon?

p.Ser504Ter chr18:55,234,435G>T ENST00000635822.2

Gene implicated in a syndromic intellectual disability; this looks like a stop-gain.
But the exon is coding only in one transcript, and it is not conserved across vertebrates.

The catch If the exon is not a real coding region, the “nonsense” call collapses — the variant is most likely benign. Always check the transcript and conservation.

The catch If the exon is not a real coding region, the “nonsense” call collapses, and the variant is most likely benign. Always check the transcript and conservation.

Try it, ▶ open the session Compare transcripts; read the 100-vertebrate conservation over this exon.

Case: Irina Giurgea, Hôpital Trousseau

TCF4 variant in a non-conserved exon on hg38 — TCF4 apparent stop-gain in a non-conserved, transcript-specific exon

Splicing

synonymous and deep-intronic variants that still break splicing

IGHMBP2 — a new splice site deep in an intron

IGHMBP2: a new splice site deep in an intron

NM_002180(IGHMBP2):c.712-610A>G hg38 chr11:68,914,208

A variant deep in an intron, far from any coding exon — easy to dismiss.
But it can create a new splice site.

A variant deep in an intron, far from any coding exon, easy to dismiss.
But it can create a new splice site.

Scan the predictors The Splicing Impact / SpliceAI track flags the gain; SpliceVarDB and a PubTator hit corroborate it.

Try it, ▶ open the session Turn on Splicing Impact; inspect the SpliceAI delta scores at the variant.

Session: s/Max/ighmbp2.712 · PMID 33189025

IGHMBP2 deep-intronic splice variant on hg38 — IGHMBP2 deep-intronic variant with SpliceAI / Splicing Impact

KCTD7 — a synonymous variant that isn't silent

KCTD7: a synonymous variant that isn't silent

KCTD7:c.456G>A p.Val152Val exon 3

A synonymous change — no amino-acid change, so it looks harmless.
But it disrupts splicing.

A synonymous change with no amino-acid change, so it looks harmless.
But it disrupts splicing.

Synonymous ≠ silent The Splicing Impact track shows the effect; the variant is in the LOVD of a 2019 paper from the same lab.

Try it, ▶ open the session Check the splicing predictions over this synonymous position.

Session: s/Max/kctd7.456GA · PMC10506157

KCTD7 c.456G>A synonymous splice-affecting variant on hg38 — KCTD7 synonymous variant predicted to affect splicing

Non-coding & regulatory

enhancers, promoters and RNA genes

POU1F1 — a deletion upstream of the gene

POU1F1: a deletion upstream of the gene

8.7 kb deletion, ~3 kb upstream hg38 chr3:87,279,612-87,288,322

Homozygous deletion upstream of POU1F1, a pituitary transcription factor (pituitary hormone deficiency).
No coding sequence is touched — the evidence is regulatory.

Homozygous deletion upstream of POU1F1, a pituitary transcription factor (pituitary hormone deficiency).
No coding sequence is touched, so the evidence is regulatory.

Read the regulation The deletion removes an ENCODE cCRE with a distal-enhancer signature; conservation and GTEx (pituitary +++) support its role.

Try it, ▶ open the session Turn on ENCODE cCREs, 100-vertebrate conservation, and GTEx over the deleted region.

Case: Amselem & Legendre labs, Hôpital Trousseau

POU1F1 upstream regulatory deletion on hg38 — POU1F1 upstream deletion overlapping a distal-enhancer cCRE

SHH / ZRS — a limb enhancer in an intron of LMBR1

SHH / ZRS: a limb enhancer in an intron of LMBR1

Patient chr7:156,791,472C>T intron 5 of LMBR1 (the ZRS)

The ZRS is a classic long-range enhancer of SHH; variants in it cause limb malformations.
In snakes, a 17 bp ZRS deletion contributed to limb loss (Kvon et al.).

Motif in an enhancer BLAT the snake sequence and Short Match the ETS1 motif; the patient variant sits in a conserved ETS motif inside a distal-enhancer cCRE, with other OMIM-allele patients nearby.

Try it, ▶ open the session Use BLAT / Short Match for the ETS motif; read the cCRE, conservation and OMIM alleles.

Cases: Wieczorek et al. 2009; snake example: Kvon et al.

SHH ZRS enhancer variant in LMBR1 intron 5 on hg38 — The ZRS limb enhancer with ETS motif, cCRE and conservation

RNU4-2 — a variant in a non-coding RNA gene

RNU4-2: a variant in a non-coding RNA gene

hg38 chr12:120,291,858 C>T RNU4-2 (NR_003137.3):n.46G>A

RNU4-2 encodes the U4 spliceosomal snRNA — a non-coding RNA gene, not a protein.
Recently (2024) shown to cause one of the most common monogenic neurodevelopmental disorders (ReNU syndrome).

RNU4-2 encodes the U4 spliceosomal snRNA, a non-coding RNA gene, not a protein.
Recently (2024) shown to cause one of the most common monogenic neurodevelopmental disorders (ReNU syndrome).

No protein here There is no coding consequence to read; you reason from the RNA gene itself and the recent literature.

Try it, ▶ open the session View the variant within the RNU4-2 gene body; a second hotspot sits at n.129G>A.

Case: Jon Bernstein · medRxiv 2025

RNU4-2 snRNA-gene variant on hg38 — RNU4-2 non-coding RNA-gene variant on hg38

Structural & repeat

CNVs and repeat expansions

A 2.22 Mb duplication on chromosome 22

chr22:g.18,895,798-21,111,753dup GRCh38 2.22 Mb

A large copy-number gain at 22q11.2 — a different interpretation problem from SNVs.
Load the CNV Recommended Track Set.

CNV-specific evidence ClinGen Dosage (triplosensitivity), ClinVar CNVs, DECIPHER and PanelApp CNV regions — each filterable.

A large copy-number gain at 22q11.2, a different interpretation problem from SNVs.
Load the CNV Recommended Track Set.

CNV-specific evidence ClinGen Dosage (triplosensitivity), ClinVar CNVs, DECIPHER and PanelApp CNV regions, each filterable.

Try it, ▶ open the session Load the CNV RTS; compare the duplication against ClinGen Dosage and DECIPHER.

Example session

Session: s/Lou/clinGenCNVsDupExample

chr22 2.22 Mb duplication on hg38 — A 2.22 Mb duplication with ClinGen Dosage, ClinVar CNVs, DECIPHER and PanelApp

FGF14 — a GAA repeat expansion

FGF14: a GAA repeat expansion

FGF14 intron 1 hg38 chr13:102,161,567 ~270-300 GAA repeats

Late-onset cerebellar ataxia (SCA27B) caused by an intronic repeat expansion — not an SNV or CNV.
A distinct class of variant with its own resources.

Late-onset cerebellar ataxia (SCA27B) caused by an intronic repeat expansion, not an SNV or CNV.
A distinct class of variant with its own resources.

A third variant class View the intron-1 GAA locus in the Browser, then cross-check dedicated tandem-repeat resources (WebSTR, TRatlas).

Try it, ▶ open the session Navigate to the intron-1 repeat; compare against the tandem-repeat tracks/resources.

Session: s/Max/fgf14

FGF14 GAA repeat-expansion locus on hg38 — FGF14 intron-1 GAA repeat locus on hg38

More cases

a gallery of de novo neurodevelopmental variants

More cases: de novo neurodevelopmental variants

A gallery of further worked cases (GSS series) — each opens as a live session:

A gallery of further worked cases (GSS series), each opening as a live session:

LRRC8A c.730T>C p.Phe244Leu — multisystem disorder, de novo heterozygous. session
KPNA4 c.557G>A p.Gly186Asp chr3:160,526,107C>T — seizures, developmental delay, autism. session
ERCC8 c.550+2T>C splice + a complex maternal SV — compound heterozygous, Cockayne-spectrum. session
RNU4ATAC n.12C>T + n.120T>G — minor-spliceosome snRNA, compound heterozygous, multisystem.
LRRC8A c.730T>C p.Phe244Leu, multisystem disorder, de novo heterozygous. session
KPNA4 c.557G>A p.Gly186Asp chr3:160,526,107C>T, seizures, developmental delay, autism. session
ERCC8 c.550+2T>C splice + a complex maternal SV, compound heterozygous, Cockayne-spectrum. session
RNU4ATAC n.12C>T + n.120T>G, minor-spliceosome snRNA, compound heterozygous, multisystem.

Same recipe Different genes and mechanisms, one workflow: open the session, load the right track set, read the evidence.

What these cases show

Coding variants can be read almost off the tracks — but always check the transcript and conservation (TCF4).
Synonymous and deep-intronic variants can still break splicing — scan the splicing predictors.
Coding variants can be read almost off the tracks, but always check the transcript and conservation (TCF4).
Synonymous and deep-intronic variants can still break splicing, so scan the splicing predictors.
Non-coding variants are interpreted from regulatory context: cCREs, conservation, expression, TF motifs.
CNVs and repeat expansions are their own classes, each with dedicated tracks and resources.

The habit Turn every variant into a set of questions, then let the right track answer each one.

Thank you!

Questions? · genome@soe.ucsc.edu

UCSC Genome Browser · genome.ucsc.edu