Is ANKRD29 p.Asp38Val (c.113A>T) pathogenic?

ANKRD29 p.Asp38Val (c.113A>T) is classified Uncertain significance in ANKRD29 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-06). AlphaMissense: ambiguous (0.4506); Ultra-rare (popmax 0.0213%, afr).

How common is ANKRD29 p.Asp38Val (c.113A>T) in the general population?

ANKRD29 p.Asp38Val (c.113A>T) is ultra-rare (popmax 0.0213%, afr) (gnomAD).

What do computational predictors say about ANKRD29 p.Asp38Val (c.113A>T)?

AlphaMissense predicts ambiguous (score 0.4506) — an in-silico prediction, not a clinical call.

ANKRD29 p.Asp38Val

c.113A>T · rs368282337 · VCV3124837

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4506 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0213%, afr)

Computational evidence

Protein change
AlphaMissense	0.4506	ambiguous
REVEL	0.606	indeterminate
SaProt	LLR -8.54	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.3, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 62 kb · p 0.28 · regional, not allelic
Overall
CADD	28.7	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0213% African / African-American · 16/75,062 alleles

Filtering AF 0.0133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0109%

Overall 0.00279% 45/1,614,162 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0213%	4,691
South Asian	0.0154%	6,506
Remaining individualsnot grpmax-eligible	0.0128%	7,812
East Asian	0.00891%	11,222
European (non-Finnish)	0.000254%	393,334

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: ANKRD29
Protein: p.Asp38Val
Coding: c.113A>T
MANE Select: NM_173505
dbSNP: rs368282337
Type: single nucleotide variant
Location: chr18:23649102 (GRCh38)
Gene constraint: LOEUF 1.187 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.86

Full ANKRD29 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANKRD29 p.Ala103Thr Uncertain significance ★ same type
ANKRD29 p.Ala185Pro Uncertain significance ★ ⚠ same type
ANKRD29 p.Ala202Val Uncertain significance ★ same type
ANKRD29 p.Ala249Val Uncertain significance ★ ⚠ same type
ANKRD29 p.Ala260Val Uncertain significance ★ ⚠ same type
ANKRD29 p.Ala280Thr Uncertain significance ★ ⚠ same type
ANKRD29 p.Ala280Val Uncertain significance ★ ⚠ same type
ANKRD29 p.Arg200Gly 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/ankrd29-p-asp38val (accessed [today's date]).

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