Is USH2A p.Ser5144= (c.15432C>T) pathogenic?

USH2A p.Ser5144= (c.15432C>T) is classified Likely benign in USH2A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-17). Very rare (popmax 0.00666%, afr); Associated with Usher syndrome type 2A.

What condition is associated with USH2A p.Ser5144= (c.15432C>T)?

USH2A p.Ser5144= (c.15432C>T) is associated with Usher syndrome type 2A (ClinVar).

How common is USH2A p.Ser5144= (c.15432C>T) in the general population?

USH2A p.Ser5144= (c.15432C>T) is very rare (popmax 0.00666%, afr) (gnomAD).

USH2A p.Ser5144=

c.15432C>T · rs145362017 · VCV793968

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00666%, afr)

Conditions

Usher syndrome type 2A

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.56 · evaluated, not missing
Constraint at this position
Conservation	phyloP -2.8	GERP -4.4
Overall
CADD	4.058	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00666% African / African-American · 5/75,042 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00202%

Overall 0.00279% 45/1,614,142 alleles · very rare exomes 40/1,461,872 · genomes 5/152,270 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00666%	15,008
South Asian	0.00329%	30,359
European (non-Finnish)	0.00314%	31,893

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: USH2A
Protein: p.Ser5144=
Coding: c.15432C>T
MANE Select: NM_206933
dbSNP: rs145362017
Type: single nucleotide variant
Location: chr1:215628901 (GRCh38)
Gene constraint: LOEUF 0.855 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

Full USH2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Usher syndrome type 2A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

USH2A c.12295-3T>A Pathogenic ★★★ same condition
USH2A c.8559-2A>G Pathogenic ★★★ same condition
USH2A c.8682-9A>G Pathogenic ★★★ same condition
USH2A p.Ala4740Asp Pathogenic ★★★ ⚠ same condition
USH2A p.Arg3905Cys Pathogenic ★★★ ⚠ same condition
USH2A p.Arg4192Cys Likely pathogenic ★★★ ⚠ same condition
USH2A p.Asn346His Pathogenic ★★★ same condition
USH2A p.Asn4292Asp Likely pathogenic ★★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ush2a-p-ser5144 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown