Is HAGH p.Ala15Val (c.44C>T) pathogenic?

HAGH p.Ala15Val (c.44C>T) is classified Uncertain significance in HAGH (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-22). AlphaMissense: likely benign (0.1388); No allele count reported in gnomAD v4.1 (AN 1,189,724).

How common is HAGH p.Ala15Val (c.44C>T) in the general population?

HAGH p.Ala15Val (c.44C>T) is no allele count reported in gnomAD v4.1 (AN 1,189,724) (gnomAD).

What do computational predictors say about HAGH p.Ala15Val (c.44C>T)?

AlphaMissense predicts likely benign (score 0.1388) — an in-silico prediction, not a clinical call.

HAGH p.Ala15Val

c.44C>T · rs1037815745 · VCV3104147

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1388 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,189,724)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1388	likely benign
REVEL	0.201	benign-leaning
SaProt	LLR -6.48	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 2.3	GERP 0.22, phastCons 0.056
Regional constraint	o/e 1.14	unconstrained · MANE · 18 kb · p 0.0043 · regional, not allelic
Overall
CADD	13.27	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

No allele count reported in gnomAD v4.1 (AN 1,189,724). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: HAGH
Protein: p.Ala15Val
Coding: c.44C>T
MANE Select: NM_005326
dbSNP: rs1037815745
Type: single nucleotide variant
Location: chr16:1826744 (GRCh38)
Gene constraint: LOEUF 1.403 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.57 · 2 PDB

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

Similar variants

HAGH p.Ala187Val Uncertain significance ★ ⚠ same type
HAGH p.Ala18Val Uncertain significance ★ ⚠ same type
HAGH p.Ala264Thr Uncertain significance ★ ⚠ same type
HAGH p.Ala284Thr Uncertain significance ★ ⚠ same type
HAGH p.Arg232His Uncertain significance ★ ⚠ same type
HAGH p.Arg242Trp Uncertain significance ★ ⚠ same type
HAGH p.Arg294Gln Uncertain significance ★ ⚠ same type
HAGH p.Arg297His Uncertain significance ★ ⚠ same type

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/hagh-p-ala15val (accessed [today's date]).

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