Is EXPH5 p.Ser902Pro (c.2704T>C) pathogenic?

EXPH5 p.Ser902Pro (c.2704T>C) is classified Uncertain significance in EXPH5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-06). AlphaMissense: likely benign (0.0814); Ultra-rare (popmax 0.02%, afr); Associated with Inborn genetic diseases.

What condition is associated with EXPH5 p.Ser902Pro (c.2704T>C)?

EXPH5 p.Ser902Pro (c.2704T>C) is associated with Inborn genetic diseases (ClinVar).

How common is EXPH5 p.Ser902Pro (c.2704T>C) in the general population?

EXPH5 p.Ser902Pro (c.2704T>C) is ultra-rare (popmax 0.02%, afr) (gnomAD).

What do computational predictors say about EXPH5 p.Ser902Pro (c.2704T>C)?

AlphaMissense predicts likely benign (score 0.0814) — an in-silico prediction, not a clinical call.

EXPH5 p.Ser902Pro

c.2704T>C · rs373483398 · VCV3091243

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0814 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.02%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0814	likely benign
REVEL	0.066	moderately benign-leaning
SaProt	LLR -7.18	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP -2, phastCons 0.99
Regional constraint	o/e 0.99	unconstrained · MANE · 84 kb · p 0.73 · regional, not allelic
Overall
CADD	15.22	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.02% African / African-American · 15/74,940 alleles

Filtering AF 0.0123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00989%

Overall 0.00105% 17/1,614,050 alleles · ultra-rare exomes 8/1,461,846 · genomes 9/152,204 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.02%	4,996
Admixed American	0.00167%	59,990
Remaining individualsnot grpmax-eligible	0.0016%	62,486

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: EXPH5
Protein: p.Ser902Pro
Coding: c.2704T>C
MANE Select: NM_015065
dbSNP: rs373483398
Type: single nucleotide variant
Location: chr11:108512803 (GRCh38)
Gene constraint: LOEUF 1.142 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 36.39
Residue 902: the 'disordered' region

Full EXPH5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EXPH5 p.Ser902Cys Uncertain significance ★ ⚠ same residue
EXPH5 p.Ala1429Ser Uncertain significance ★★ ⚠ same condition
EXPH5 p.Arg1727Lys Uncertain significance ★★ ⚠ same condition
EXPH5 p.Asn1548Asp Uncertain significance ★★ ⚠ same condition
EXPH5 p.Asp741His Uncertain significance ★★ ⚠ same condition
EXPH5 p.Gln1464Arg Uncertain significance ★★ ⚠ same condition
EXPH5 p.Gly54Arg Uncertain significance ★★ ⚠ same condition
EXPH5 p.Leu1519Arg Uncertain significance ★★ ⚠ 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/exph5-p-ser902pro (accessed [today's date]).

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