Is CCDC62 p.Asp488Asn (c.1462G>A) pathogenic?

CCDC62 p.Asp488Asn (c.1462G>A) is classified Uncertain significance in CCDC62 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-01). AlphaMissense: likely benign (0.0919); Very rare (popmax 0.000657%).

How common is CCDC62 p.Asp488Asn (c.1462G>A) in the general population?

CCDC62 p.Asp488Asn (c.1462G>A) is very rare (popmax 0.000657%) (gnomAD).

What do computational predictors say about CCDC62 p.Asp488Asn (c.1462G>A)?

AlphaMissense predicts likely benign (score 0.0919) — an in-silico prediction, not a clinical call.

CCDC62 p.Asp488Asn

c.1462G>A · rs1301334181 · VCV2395248

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0919 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000657%)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0919	likely benign
REVEL	0.138	moderately benign-leaning
SaProt	LLR -5.42	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 3.2	GERP -3, phastCons 0.57
Regional constraint	o/e 0.87	unconstrained · MANE · 49 kb · p 0.00021 · regional, not allelic
Overall
CADD	19.02	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000657%

Overall 0.000657% 1/152,176 alleles · very rare

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.Asp488Asn
Coding: c.1462G>A
MANE Select: NM_201435
dbSNP: rs1301334181
Type: single nucleotide variant
Location: chr12:122801608 (GRCh38)
Gene constraint: LOEUF 1.012 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.07
Residue 488: a UniProt-annotated variant site (in spgf67)

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

Similar variants

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
CCDC62 p.Arg11Cys 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-asp488asn (accessed [today's date]).

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