Is ANKAR p.Thr682Ala (c.2044A>G) pathogenic?

ANKAR p.Thr682Ala (c.2044A>G) is classified Benign in ANKAR (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-03). AlphaMissense: likely benign (0.0914); Low-frequency (popmax 1.87%, afr).

How common is ANKAR p.Thr682Ala (c.2044A>G) in the general population?

ANKAR p.Thr682Ala (c.2044A>G) is low-frequency (popmax 1.87%, afr) (gnomAD).

What do computational predictors say about ANKAR p.Thr682Ala (c.2044A>G)?

AlphaMissense predicts likely benign (score 0.0914) — an in-silico prediction, not a clinical call.

ANKAR p.Thr682Ala

c.2044A>G · rs147390101 · VCV783346

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0914 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.87%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0914	likely benign
REVEL	0.055	moderately benign-leaning
SaProt	LLR -4.04	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 5	GERP 0.13, phastCons 0.39
Regional constraint	o/e 0.93	unconstrained · MANE · 70 kb · p 0.0059 · regional, not allelic
Overall
CADD	14.42	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 1.87% African / African-American · 1,404/74,902 alleles

Filtering AF 1.79% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.76%

Overall 0.126% 2,021/1,609,792 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.87%	53
Middle Eastern	0.413%	242
Admixed American	0.258%	388
Remaining individualsnot grpmax-eligible	0.21%	476
Ashkenazi Jewishnot grpmax-eligible	0.118%	844
European (non-Finnish)	0.023%	4,345
South Asian	0.00222%	45,133

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: ANKAR
Protein: p.Thr682Ala
Coding: c.2044A>G
MANE Select: NM_001378068
dbSNP: rs147390101
Type: single nucleotide variant
Location: chr2:189707071 (GRCh38)
Gene constraint: LOEUF 1.07 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.79

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

Similar variants

ANKAR p.Asn938= Benign ★★ same type
ANKAR p.Gln1419Leu Benign ★★ same type
ANKAR p.Ile1349= Benign ★★ same type
ANKAR p.Leu94Arg Benign ★★ same type
ANKAR p.Thr206Ala Benign ★★ same type
ANKAR p.Thr92= Benign ★★ same type
ANKAR p.Tyr1262Ser Benign ★★ same type
ANKAR p.Val776Ala Likely benign ★★ ⚠ 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/ankar-p-thr682ala (accessed [today's date]).

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