Is ANKDD1B p.Ala60Asp (c.179C>A) pathogenic?

ANKDD1B p.Ala60Asp (c.179C>A) is classified Benign in ANKDD1B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). AlphaMissense: likely benign (0.1166); Low-frequency (popmax 4.85%, afr).

How common is ANKDD1B p.Ala60Asp (c.179C>A) in the general population?

ANKDD1B p.Ala60Asp (c.179C>A) is low-frequency (popmax 4.85%, afr) (gnomAD).

What do computational predictors say about ANKDD1B p.Ala60Asp (c.179C>A)?

AlphaMissense predicts likely benign (score 0.1166) — an in-silico prediction, not a clinical call.

ANKDD1B p.Ala60Asp

c.179C>A · rs79228722 · VCV774178

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1166 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 4.85%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.1166	likely benign
SaProt	LLR -6.49	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.14	GERP -0.54, phastCons 0.008
Regional constraint	o/e 1.04	unconstrained · MANE · 24 kb · p 0.48 · regional, not allelic
Overall
CADD	16.45	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 4.85% African / African-American · 3,127/64,522 alleles

Filtering AF 4.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.65%

Overall 0.322% 3,971/1,231,902 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.85%	21
Middle Eastern	1.12%	89
Admixed American	0.573%	174
Remaining individualsnot grpmax-eligible	0.491%	203
European (non-Finnish)	0.0442%	2,261
Ashkenazi Jewishnot grpmax-eligible	0.0168%	5,954
Finnishnot grpmax-eligible	0.0126%	7,946
South Asian	0.0123%	8,105

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: ANKDD1B
Protein: p.Ala60Asp
Coding: c.179C>A
MANE Select: NM_001276713
dbSNP: rs79228722
Type: single nucleotide variant
Location: chr5:75611813 (GRCh38)
Gene constraint: LOEUF 1.173 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.90

Full ANKDD1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANKDD1B p.Arg470His Benign/Likely benign ★★ same type
ANKDD1B p.Asn318Lys Benign ★★ same type
ANKDD1B p.Asp2Glu Benign ★★ same type
ANKDD1B p.Gln462Ter Likely benign ★★ same type
ANKDD1B p.His245Arg Benign ★★ same type
ANKDD1B p.Leu495Val Benign ★★ ⚠ same type
ANKDD1B p.Trp463Ter Benign ★★ same type
ANKDD1B p.Val292Ala 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/ankdd1b-p-ala60asp (accessed [today's date]).

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