Is PSPH p.Asn124= (c.372T>C) pathogenic?

PSPH p.Asn124= (c.372T>C) is classified Likely benign in PSPH (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-09). Absent from gnomAD v4.1; Associated with PSPH deficiency.

What condition is associated with PSPH p.Asn124= (c.372T>C)?

PSPH p.Asn124= (c.372T>C) is associated with PSPH deficiency (ClinVar).

How common is PSPH p.Asn124= (c.372T>C) in the general population?

PSPH p.Asn124= (c.372T>C) is absent from gnomAD v4.1 (gnomAD).

PSPH p.Asn124=

c.372T>C · rs2534872061 · VCV2017385

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

PSPH deficiency

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 -0.31	GERP -3.8
Overall
CADD	0.485	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PSPH
Protein: p.Asn124=
Coding: c.372T>C
MANE Select: NM_004577
dbSNP: rs2534872061
Type: single nucleotide variant
Location: chr7:56017283 (GRCh38)
Gene constraint: LOEUF 1.063 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.88 · 6 PDB

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

Disease context

PSPH deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PSPH p.Asn124Ser Uncertain significance ★★ ⚠ same residue
PSPH p.Asn124His Uncertain significance ★ ⚠ same residue
PSPH p.Arg101Ter Likely pathogenic ★★ same condition
PSPH c.422-3A>C Uncertain significance ★★ same condition
PSPH c.570+3A>G Uncertain significance ★★ same condition
PSPH c.570+5G>C Uncertain significance ★★ same condition
PSPH c.*341G>A Uncertain significance ★★ same condition
PSPH p.Asp32Asn 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/psph-p-asn124 (accessed [today's date]).

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