Is CCDC62 p.Arg71His (c.212G>A) pathogenic?

CCDC62 p.Arg71His (c.212G>A) is classified Uncertain significance in CCDC62 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-08). AlphaMissense: ambiguous (0.3502); Ultra-rare (popmax 0.0317%, amr).

How common is CCDC62 p.Arg71His (c.212G>A) in the general population?

CCDC62 p.Arg71His (c.212G>A) is ultra-rare (popmax 0.0317%, amr) (gnomAD).

What do computational predictors say about CCDC62 p.Arg71His (c.212G>A)?

AlphaMissense predicts ambiguous (score 0.3502) — an in-silico prediction, not a clinical call.

CCDC62 p.Arg71His

c.212G>A · VCV3264241

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3502 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0317%, amr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3502	ambiguous
REVEL	0.161	moderately benign-leaning
SaProt	LLR -7.48	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.3, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 49 kb · p 0.00021 · regional, not allelic
Overall
CADD	28.2	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 0.0317% Admixed American · 19/60,000 alleles

Filtering AF 0.0207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0172%

Overall 0.00415% 67/1,614,006 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0317%	3,158
Remaining individualsnot grpmax-eligible	0.0128%	7,812
European (non-Finnish)	0.00305%	32,776
African / African-American	0.00267%	37,513
East Asian	0.00223%	44,882
Finnishnot grpmax-eligible	0.00156%	64,026

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: CCDC62
Protein: p.Arg71His
Coding: c.212G>A
MANE Select: NM_201435
Type: single nucleotide variant
Location: chr12:122777666 (GRCh38)
Gene constraint: LOEUF 1.012 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.07

Full CCDC62 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC62 p.Arg71Cys Uncertain significance ★ ⚠ same residue
CCDC62 p.Gln364= Benign ★★ same type
CCDC62 p.Ala190Gly Uncertain significance ★ ⚠ same type
CCDC62 p.Ala271Glu Uncertain significance ★ ⚠ same type
CCDC62 p.Ala271Ser Uncertain significance ★ ⚠ same type
CCDC62 p.Ala322Asp Uncertain significance ★ ⚠ same type
CCDC62 p.Ala503Gly Uncertain significance ★ ⚠ same type
CCDC62 p.Ala6Ser 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/ccdc62-p-arg71his (accessed [today's date]).

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