Is ANKRD1 p.Val106= (c.318T>C) pathogenic?

ANKRD1 p.Val106= (c.318T>C) is classified Likely benign in ANKRD1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-07-24). Very rare (popmax 0.0033%, sas); Associated with Cardiovascular phenotype.

What condition is associated with ANKRD1 p.Val106= (c.318T>C)?

ANKRD1 p.Val106= (c.318T>C) is associated with Cardiovascular phenotype (ClinVar).

How common is ANKRD1 p.Val106= (c.318T>C) in the general population?

ANKRD1 p.Val106= (c.318T>C) is very rare (popmax 0.0033%, sas) (gnomAD).

ANKRD1 p.Val106=

c.318T>C · rs768982146 · VCV1596574

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0033%, sas)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.99	GERP -2.8, phastCons 0.021
Overall
CADD	3.257	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0033% South Asian · 3/91,002 alleles

Filtering AF 0.000876% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.00031% 5/1,613,126 alleles · very rare exomes 4/1,461,416 · genomes 1/151,710 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0033%	30,334
Admixed American	0.00167%	59,950
African / African-American	0.00134%	74,680

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: ANKRD1
Protein: p.Val106=
Coding: c.318T>C
MANE Select: NM_014391
dbSNP: rs768982146
Type: single nucleotide variant
Location: chr10:90919158 (GRCh38)
Gene constraint: LOEUF 1.038 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.64

Full ANKRD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ANKRD1 p.Val106Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
ANKRD1 c.207+1G>T Uncertain significance ★★ same condition
ANKRD1 c.27+1G>T Uncertain significance ★★ same condition
ANKRD1 c.28-3T>C Uncertain significance ★★ same condition
ANKRD1 c.651+4T>A Uncertain significance ★★ same condition
ANKRD1 c.750+2T>C Uncertain significance ★★ same condition
ANKRD1 c.750+4A>G Uncertain significance ★★ same condition
ANKRD1 c.751-3T>C 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/ankrd1-p-val106 (accessed [today's date]).

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