Is POMP p.Val38Ala (c.113T>C) pathogenic?

POMP p.Val38Ala (c.113T>C) is classified Uncertain significance in POMP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-01). AlphaMissense: likely benign (0.2361); Ultra-rare (popmax 0.0402%, amr); Associated with Inborn genetic diseases.

What condition is associated with POMP p.Val38Ala (c.113T>C)?

POMP p.Val38Ala (c.113T>C) is associated with Inborn genetic diseases (ClinVar).

How common is POMP p.Val38Ala (c.113T>C) in the general population?

POMP p.Val38Ala (c.113T>C) is ultra-rare (popmax 0.0402%, amr) (gnomAD).

What do computational predictors say about POMP p.Val38Ala (c.113T>C)?

AlphaMissense predicts likely benign (score 0.2361) — an in-silico prediction, not a clinical call.

POMP p.Val38Ala

c.113T>C · rs780481787 · VCV1437956

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2361 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0402%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2361	likely benign
REVEL	0.2	benign-leaning
SaProt	LLR -6.28	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 7.8	GERP 1.8, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 19 kb · p 0.048 · regional, not allelic
Overall
CADD	22.4	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 0.0402% Admixed American · 24/59,724 alleles

Filtering AF 0.0277% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0235%

Overall 0.00221% 35/1,581,068 alleles · ultra-rare exomes 18/1,428,990 · genomes 17/152,078 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0402%	2,488
Remaining individualsnot grpmax-eligible	0.00163%	61,300
European (non-Finnish)	0.000868%	115,168

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: POMP
Protein: p.Val38Ala
Coding: c.113T>C
MANE Select: NM_015932
dbSNP: rs780481787
Type: single nucleotide variant
Location: chr13:28664520 (GRCh38)
Gene constraint: LOEUF 1.191 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 81.76 · 11 PDB

Full POMP 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

POMP p.Val38Leu Uncertain significance ★★ ⚠ same residue
POMP p.Asn108His Uncertain significance ★★ ⚠ same condition
POMP p.Asn40Ser Uncertain significance ★★ ⚠ same condition
POMP p.Gln56His Uncertain significance ★★ ⚠ same condition
POMP p.His28Pro Uncertain significance ★★ ⚠ same condition
POMP p.Ile112Val Uncertain significance ★★ ⚠ same condition
POMP p.Leu30Phe Uncertain significance ★★ ⚠ same condition
POMP p.Leu6Pro 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/pomp-p-val38ala (accessed [today's date]).

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