Is CORO7-PAM16 p.Arg193Gln (c.578G>A) pathogenic?

CORO7-PAM16 p.Arg193Gln (c.578G>A) is classified Benign in CORO7-PAM16 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-04-19). AlphaMissense: likely benign (0.1499); Common (popmax 79.2%, eas) — too common for a highly-penetrant pathogenic allele.

What do computational predictors say about CORO7-PAM16 p.Arg193Gln (c.578G>A)?

AlphaMissense predicts likely benign (score 0.1499) — an in-silico prediction, not a clinical call.

CORO7-PAM16 p.Arg193Gln

Q: How common is CORO7-PAM16 p.Arg193Gln (c.578G>A) in the general population?

CORO7-PAM16 p.Arg193Gln (c.578G>A) is common (popmax 79.2%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.578G>A · rs3747579 · VCV1231728

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1499 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 79.2%, eas) — too common for a highly-penetrant pathogenic allele

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1499	likely benign
REVEL	0.143	moderately benign-leaning
SaProt	LLR -11.45	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.7	GERP 0.1, phastCons 0.98
Overall
CADD	26.5	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 79.2% East Asian · 35,539/44,874 alleles

Filtering AF 78.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 78.2%

Overall 68.3% 1,101,536/1,613,632 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	79.2%	1
Ashkenazi Jewishnot grpmax-eligible	72.4%	1
European (non-Finnish)	72.2%	1
Finnishnot grpmax-eligible	70.4%	1
Amishnot grpmax-eligible	66.6%	2
Remaining individualsnot grpmax-eligible	66.4%	2
Middle Eastern	65.6%	2
South Asian	58.4%	2
Admixed American	57.5%	2
African / African-American	19.5%	5

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: CORO7-PAM16
Protein: p.Arg193Gln
Coding: c.578G>A
MANE Select: NM_024535 · reported on NM_001201479
dbSNP: rs3747579
Type: single nucleotide variant
Location: chr16:4395326 (GRCh38)

Full CORO7-PAM16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/coro7-pam16-p-arg193gln (accessed [today's date]).

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